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I'm putting the finishing touches on a developer's blog post for situation 1 right now, and it should be up some time in the next week or so. Regarding 2, are your users already cookied and IDed to user records(with email addresses) in your web app? If so you can use syncLead to send the Email and the Marketo Cookie down to Marketo to quickly associate your records to Marketo's web activity tracking: http://developers.marketo.com/documentation/soap/synclead/
#1 is a little tricky. It is a big security risk if Marketo exposes lead data to external servers. So prepopulation can only happen on Marketo Landing Pages (iFramed or directly on the landing page).
For #2, I would just suggest to add an associateLead Munchkin API call when your web forms are submitted. This will make the lead known just as if they filled out a Marketo form and all past and future lead activity will be attributed to the lead in Marketo.
Information on the associateLead call can be found here: http://developers.marketo.com/documentation/websites/lead-tracking-munchkin-js/